3R1R

RIBONUCLEOTIDE REDUCTASE R1 PROTEIN WITH AMPPNP OCCUPYING THE ACTIVITY SITE FROM ESCHERICHIA COLI

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.287 
  • R-Value Observed: 0.263 

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This is version 1.2 of the entry. See complete history. 


Literature

Binding of allosteric effectors to ribonucleotide reductase protein R1: reduction of active-site cysteines promotes substrate binding.

Eriksson, M., Uhlin, U., Ramaswamy, S., Ekberg, M., Regnstrom, K., Sjoberg, B.M., Eklund, H.

(1997) Structure 5: 1077-1092

  • DOI: 10.1016/s0969-2126(97)00259-1
  • Primary Citation of Related Structures:  
    4R1R, 1R1R, 3R1R, 2R1R

  • PubMed Abstract: 

    • Ribonucleotide reductase (RNR) is an essential enzyme in DNA synthesis, catalyzing all de novo synthesis of deoxyribonucleotides. The enzyme comprises two dimers, termed R1 and R2, and contains the redox active cysteine residues, Cys462 and Cys225. The reduction of ribonucleotides to deoxyribonucleotides involves the transfer of free radicals ...

    Ribonucleotide reductase (RNR) is an essential enzyme in DNA synthesis, catalyzing all de novo synthesis of deoxyribonucleotides. The enzyme comprises two dimers, termed R1 and R2, and contains the redox active cysteine residues, Cys462 and Cys225. The reduction of ribonucleotides to deoxyribonucleotides involves the transfer of free radicals. The pathway for the radical has previously been suggested from crystallographic results, and is supported by site-directed mutagenesis studies. Most RNRs are allosterically regulated through two different nucleotide-binding sites: one site controls general activity and the other controls substrate specificity. Our aim has been to crystallographically demonstrate substrate binding and to locate the two effector-binding sites.

    Related Citations: 
    • Structure of Ribonucleotide Reductase Protein R1
      Uhlin, U., Eklund, H.
      (1994) Nature 370: 533
    Organizational Affiliation: 

    Department of Molecular Biology, Swedish University of Agricultural Sciences, Uppsala Biomedical Center, Sweden.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RIBONUCLEOTIDE REDUCTASE R1 PROTEINA, C [auth B], E [auth C]761Escherichia coliMutation(s): 0 
Gene Names: nrdA
EC: 1.17.4.1
UniProt
Find proteins for P00452 (Escherichia coli (strain K12))
Explore P00452 
Go to UniProtKB:  P00452
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
RIBONUCLEOTIDE REDUCTASE R2 PROTEINB [auth D], D [auth E], F, G [auth P]20N/AMutation(s): 0 
UniProt
Find proteins for P69924 (Escherichia coli (strain K12))
Explore P69924 
Go to UniProtKB:  P69924
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP (Subject of Investigation/LOI)
Query on ATP
Download Ideal Coordinates CCD File 
 H [auth A], I [auth B], J [auth C]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.287 
  • R-Value Observed: 0.263 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 224.61α = 90
b = 224.61β = 90
c = 336.63γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
TNTrefinement
REFMACrefinement
TNTphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-01-28
    Type: Initial release
  • Version 1.1: 2008-03-25
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance